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  How and Why You Can Create a Table of Chemical Shifts and J couplings

iNMR gives you many tools to derive the most common NMR parameters (chemical shifts and coupling constants) and a single tool where everything converges upon. This point of convergence is called the “J Manager”. Every 1D spectrum has its own manager. By default it is closed; you open it with the command: “View/J couplings” or with the easy-to-remember shortcut Cmd-J. The J manager has four main purposes:

The manager also allows for manual editing and for sorting of the parameters. When you select a line in the table, the corresponding label on the spectrum will be highlited and the splitting tree shown.

NOTE: in the following you will frequently read: “Click the extract icon”. You can also use the keyboard equivalent: e (without Cmd!).

Extracting the Js after Peak-Picking

Perform peak-picking as usual. It's important to know all the ways to create those labels, either in groups or singularly. Clic and select a region of the spectrum corresponding to a whole multiplet. If this region also contains a different peak (belonging to a different multiplet), remove the corresponding label (it's enough to click on it with the peak-picker tool). Click the “extract” icon of the J Manager. A new entry will be created at the bottom of the table. If the selection contained the correct number of frequencies, all the parameters will be extracted. In the opposite case you'll only see a “range” indication. The range does not correspond to your selection, but goes from outer peak to outer peak (= it will always be smaller).

Extracting the Js without Peak-Picking

If your selection does not contain any peak-picking label, iNMR will perform peak-picking on the fly. It's important to set a threshold, as explained elsewhere. In this way you control the number of peaks seen by the program. The result of on-the-fly peak-picking is not preserved and is not visible.

Extracting the Js from the integral regions

If no region is selected, iNMR will create a new entry for each integral region. It's as if you had selected all the integrals one by one. If a region has already been peak-picked, the frequences will be used directly. Otherwise iNMR will perform peak-picking on the fly.

Extracting the parameters with the tool “info”

This only works with singlets and doublets. Use the info-tool with the Ctrl key pressed. Your action will generate a note whose purpose, into this context, is merely to provide a visual feedback. You'll probably want to remove the note soon or later. The non-visible effect of your action is that the text of that note has also been copied into the clipboard. The second and last step is to press the “paste” icon of the J manager.

Extracting the Js from a spin system

Let's say you have simulated your spin system into a separate window. Reach that window and issue the command: “Simulate/Listing...”. Another table appears, similar to the table of the J manager. You can click into that table end edit it. For example, you may want to remove a line you are not interested into. After clicking, select all the text (Cmd-A) and copy it (Cmd-C). Return to the J Manager and paste.

Extracting the Js from the deconvolution module

It's the same old story, basically: first click the “copy” icon of the deconvolution module, then click the “paste” icon of the J Manager. In a realistic case you haven't a clean multiplet into the deconcolution module. Let's say you have two overlapped multiplets. You can follow these steps:

  1. Copy from the deconvolution module and paste into a safe place (a text document) the list of lines.
  2. Select and remove all the lines but those corresponding to the first multiplet.
  3. Click again on “copy”.
  4. Move to the J Manager and click on “paste”. You have transferred the first multiplet.
  5. Move to the text document (your safe storage), copy the text, then click on the “paste” icon of the deconvolution module. This will restore the initial situation.
  6. Repeat for all the multiplets.

Extracting the Js from 13-C spectra (decoupled)

This is the case where all signals are singlet. Perform the standard peak-picking. Select the command “Edit/Copy.../List of Peaks”. Click the “paste” icon of the deconvolution module.

Generating the Report

If you have created more entries than needed, you can remove them with the corresponding icon, after selecting them. To select non-adjacent rows, press the Cmd key. Another step you may consider is the choice among the available styles (under the menu “View”, directly below the command “J Couplings”. After you click the “report” icon, the clipboard contains your report. The multiplets are sorted in order of decreasing chemical shift and the icon “Undo” becomes dimmed. You can try with more styles until you find the one that better satisfies you. Your preference remains stored into the computer. If you have chosen a RTF style, you can hack a little. For example, the following methyl will appear in bold face: {\b CH3}.

Connection with the Plot

If you select a row into the table, the corresponding label appears selected into the plot. If you select a label, the corresponding row is conversely selected. To select more labels use a Shift-click. The Shift-click into the table extends the selection. To select non-adjacent rows, use the Cmd-click. When a row is selected, press the icon “reveal” to show the corresponding multiplet (expanded) in the plot. You may notice that the most comfortable column to click into is the right-most one, because it's not editable. Once one or more rows are selected, clicking the icon "graph" creates special annotations on the spectrum to visualize the splitting tree.

Adding Consistency

When a multiplet A is coupled with a multiplet B, their mutual coupling must be unique, yet the splitting measured at A is seldom identical to the splitting measured at B. Sometimes one measure is more reliable than the other. For example, if A is a methyl and B a methyne coupled both with A and with more nuclei, A will give a sharp and intense doublet, while B will give a weak multiplet. Quite likely, the coupling measured from the doublet will be more accurate. In this case, you can manually edit the row corresponding to B and set the constant equal to the more accurate value.
When the accuracy of the two measures is similar, you will create a consistent table if you set values equal to their average, In this way not only you respect the theory and the logic, you also increase the precision of the measure and help a future reader to spot the coupling partners. Doing it with iNMR is handy. Select the two rows (with Cmd-click), then click the icon “match”. (To undo press TWICE the icon “undo”). Even if each row contains many coupling constants, iNMR can automatically find the matching values.

don't rely on the bottom view

The bottom of the J manager reads: “clipboard=”. It's only updated after the following circumstances: you open the manager, you click either the report or the paste icon, you switch from another application, you select one of the specialized copy commands from the main “Edit” menu.

don't trust in the computer

If you change the scale reference after extracting the chemical shifts, they will remain uncorrect!. Start using the J Manager only after the spectrum has been perfectly processed.
The internal algorithms of iNMR, so far, believe that all nuclei have spin 1/2. When you see an hydrogen coupled to 14-N or deuterium, it's necessary that you enter the description of the multiplet manually, that is, using the keyboard.
When a coupling constant is small, it is necessary to resort to a resolution enhancement, otherwise the peak-picking cannot find all the lines. After you have extracted the couplings, you can remove peak-picking and/or resolution enhancement without affecting the extracted values.

See also

Spotlight Support


Undoing your Operations inside iNMR